Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatctaacggatcaggagtctcgcttgtacgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaattgtttattgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG

Basic information

species Zea mays
transcript GRMZM2G093316_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 3
taatctaacggatcaggagtc--tcgcttgtacgcttgcac--gtaaggccccattgcacagtagtcatcgcctattttaattgtttattgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
  |||    |  |   | | |  |  ||  |    | | ||   | |  |    || | |   |    |    || | ||||| | |   ||||| | | ||||||| ||||||||||||||||| ||||||||||| || ||||||||||| |||||||||||||||||||||||||| ||| |||| |||
-tatcctttgagtagtgtgccactgactattttattaggactgatcatcctttgtttctcttcaaatttgatataatataattctct---gtcatttgtatcagTGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAG

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 2
----taatcta---acggatcaggagtctcgcttgtacgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaattgtttattgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
    |  | |      |||| |    | |   || |     ||||   ||| ||   |  |    || |  |  | || || || |   | |  | ||||||   || ||    ||||| |||||||| ||||||||||| || ||||| || |||||| |||||||||  ||||||||  | || ||  |||| 
ttcatgctttgtgtgtggattatctttatgttttttttttctgcat-caagtccttttaacttcttaattgtgacttagttcaact---tctgatgatctat---agAGAATGTGGTGAGATGTGTGCAATGAAGGAGGTAACCCTTTTTTCTGATGATGCTAAATCAAGGGAAAGTGCGCAGCAACTTGGCCAA

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 2
-----------taatctaacggatcaggagtctcgcttgtacgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaa-ttgttt------attgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
           | | | ||  | ||  || | |    || |    |     | |  |         || ||||     | | || ||| ||||||      | |||  ||   |  || || |  |||||||||||||| ||||| ||||| ||||| || ||||||||| | ||||| ||||||||||| || ||  |    |||
gtatgtgcttgtgaccaaa-agttcttgattatattatgaagaaatcttttttatacttttaaatccattagtttatacatcttataaattgtttggttaaaatgttgtcctgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTGTTTTCAGATGATGCCAAATCTAAAGAAAGTGCTAAGCAATTAATGCAG

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 2
-taatctaacggatcaggagtctcgct-tgtacgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaattgtttattgtcatctatttca--gTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
 |  |||  ||  |   | |||||    |||  |||  |    |      ||||  | |||  || ||   ||  |    | |   ||  | |||  | ||  |||| |  ||||| |||||||| ||||||||||| |||||||| ||||||||| |||||||||  ||||||||  |||| ||  |||| 
ttgttctgtcgttt---gtgtctcaaggtgtgggctatctatcatttgtgcattaaatagtt-tcttcttttacatctgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 3
-------------------------taatctaacggatcaggagtctcgcttgtacgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaattgtttattgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
                         | ||   |      || | |||   || |||  ||  |   |       || |||   ||   || |  |  || || ||||    || || | |   || || |  |||||||||||||| ||||| ||||| |||||||| ||||||||| | ||||| ||||| ||||| || ||  |    |||
gtatgtgcttttgaccagaagttcttgattatattatgaagaaatcttttttctacttttaaatccattagtgtat-gcatcttataaattgtttggttaaaatgtt----gttatgtgt---agGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTTTTTTCAGATGATGCCAAATCTAAAGAGAGTGCTAAGCAATTAATGCAG

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 5
-taatctaacggatcaggagtctcgcttgta---cgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaattgtttattgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
 |  | |    |       ||   | || |    |  | |  | | |       ||      ||    |    |  |||| || |   || | ||| ||   ||||| |  ||||| |||||||| ||||||||||| |||||||| ||||||||| |||||||||  ||||||||  |||| ||  |||| 
ctgttgtttttgtctcaaggtgcgggttatctatcattcgtgcattaaatagtttttacttttacatctgatttgatttagtt-taacttctgatccat---agTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 2
taatctaacggatcaggagtctcgcttgtacgcttgcacgtaaggccccattgcacagtagtcat----cgcctattttaattgtttattgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
      ||| |||  |   |||       |   |     | |   | | | ||     |    ||    | ||| |||| || | |||| ||  |||   ||||||| |  || || |||||||| ||||| ||||||||||| | ||||||||||||||| ||||  || |||||| ||||  || | || 
---ataaactgatttgttctcttcacaaaatattgaataggagaactcaaatgttatatttctatgtcacccctgttttgatcggttat-gttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
--taatctaacggatcag--gagtctcgcttgtacgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaattgtttattgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
  ||   || |  | ||   || |  ||  |  | | ||  |  |   |  |  ||  || | | |  | || ||| |  ||| | |||| |   ||  || ||||| |  |||||||||||||| ||||||||||| || || || ||||||||| | || ||||| ||||||||||||||| || | || 
cttatgatatctaagcaattgatttgcgactccatgtttttaaatgttgatctttt--actggatttgt-gcatatct-gattttatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0025g03850.t01 (Vitis vinifera), 3'ss of exon 1
taatctaacggatcaggagtctcgcttgtacgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaattgtttattgtcatct------atttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
       |  | |      | ||  ||  |     |||            |    || || || |      | | | || ||| || || | |      | || ||||| |  || || |||||||| ||||||||||||||  | || ||||||||| | || ||||| ||||||||| | |||||| |||| 
------gattgcttgcatttgtctatttaatttaagcaatctgctatttctcatgcattattctttataattctgactttttttttttcttttgcttggactttagTGAAAGTGGGGAGATGTGTGCAATGAAGGAGGTTACATTATTTTCAGATGATGCGAAGTCAAAGGAAAGTGCACAGCAGCTGGGCCAA

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 4
taatctaacggatcaggagtctcgcttgtacgcttgcacgtaaggccccattgc----acagtagtcatcgcctattttaattgtttattgtcatct--atttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
      |  |  |        | |  | |    ||  | | ||    | ||| |     || || || |    ||| | | || |||  | |    |  | || ||||| |  || || |||||||| ||||||||||||||  | || ||||||||| | || ||||| ||||||||| | |||||| |||| 
-----cagtgattgcttgcatttgtctatttagtt-taagcaatctgctatttctcatgcattattctttatatatctgactttttttcttttgcttggactttagTGAAAGTGGGGAGATGTGTGCAATGAAGGAGGTTACATTATTTTCAGATGATGCGAAGTCAAAGGAAAGTGCACAGCAGCTGGGCCAA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211515221|gb|FL355394.1|FL355394
EST:     AAACTGATTGGCCGTGGGACATTTGGCCATGTATATGCTGGTTTTAACAG                         TGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGA
genomic: AAACTGATTGGCCGTGGGACATTTGGCCATGTATATGCTGGTTTTAACAGgtatgccttt ... tctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccccattgcacagtagtcatcgcctattttaattgtttattgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
                          ttttaat  putative branch site (score: 3)
                                             tctatttc  putative PPT
                        tattttaattgtttat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatctaacggatcaggagtctcgcttgtacgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaattgtttattgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG